Computational Biology and Bioinformatics
Ana M Rojas
The Computational Biology and Bioinformatics lab is composed by a team of Biologists, Bioinformaticians, and engineers that use computational methods, to try to understand 1) how proteins evolve and acquire novel functions, 2) how mutations impact a given protein function, and 3) how is the relationship between molecular evolution and phenotypic evolution.
Our main interests deal with protein evolution (#ProtEvol) and its relationship with structure/function (#StruFunct) in the context of signaling pathways (#SigPath).
To illustrate these concepts, we have for instance identified novel roles and residues involved in functional specificity for the RAS superfamily of proteins (Rojas et al, 2012, J. cell Biol. [PMID:22270915]), described the making-up of the human DNA Damage Response pathway (Arcas et al, Mol. Biol. Evol., 2014, [PMID: 24441036], and discovered a novel Mistmatch Repair pathway in prokaryotes (Figure down- Castañeda et al, 2017, Nat. Comm [DOI:10.1038/ncomms14246]).
In the same line we have collaborated extensively with experimental groups to describe the mitochondrial role of EXD2 (Silva et al, 2018, Nat. Cell Biol. [PMID: 29335528]) or analysed in detail the role of particular residues mutated in patient samples (Trsitan-Calvijo et al, 2016, Mov. Disords [PMID 27477325]).
We are also interested on the large-scale integration (#Integration) of transcriptomics, genomics and epigenomics data to address hypothesis-driven biological problems, as well as biomedical questions of interest. To this purpose we have designed Bioinformatics tools (Andres-Leon, 2016, Sci. Rep. [PMID:27167008]) that have been applied to identify mRNA-miRNA signatures in tumors relevant to survival. The underlying concept is to use the “pair of molecules” (mRNA-miRNA) instead the single molecule (mRNA or miRNA) to indetify tumor-type specific pairs relevant to response to survival (Figure down [Andres-Leon et al, 2017, Sci. Rep. [PMID: 28387377]).